[Bioc-devel] Biobase: Imports repeats Depends

Hervé Pagès hpages at fredhutch.org
Tue Apr 28 03:45:20 CEST 2015

Hi Henrik,

I know it's not necessary and I know that the WRE manual and
'R CMD check' don't like this but I like to list in Imports what
I import and to list in Depends what I want to see attached to
the search() path. For the same reason that I like to explicitly
export the generic functions that I define in my packages even
if exporting the methods defined on these generics is enough
(because it has the side effect to automatically export the

More generally it's about expressing intentions directly versus
expressing them in an indirect manner (e.g. by relying on side
effects). I think the latter is wrong. Hope that makes sense.


On 04/25/2015 01:12 PM, Henrik Bengtsson wrote:
> It seems unnecessary that BiocGenerics have the same package under
> Imports as under Depends.  The former can be dropped.
>> packageDescription("BiocGenerics")
> Package: BiocGenerics
> Title: S4 generic functions for Bioconductor
> Description: S4 generic functions needed by many Bioconductor packages.
> Version: 0.14.0
> Author: The Bioconductor Dev Team
> Maintainer: Bioconductor Package Maintainer
>          <maintainer at bioconductor.org>
> biocViews: Infrastructure
> Depends: methods, utils, graphics, stats, parallel
> Imports: methods, utils, graphics, stats, parallel
> Suggests: Biobase, S4Vectors, IRanges, GenomicRanges, AnnotationDbi,
>          oligoClasses, oligo, affyPLM, flowClust, affy, DESeq2, MSnbase,
>          annotate, RUnit
> License: Artistic-2.0
> Collate: S3-classes-as-S4-classes.R normarg-utils.R update-utils.R
>          .....
> NeedsCompilation: no
> Packaged: 2015-04-17 03:42:27 UTC; biocbuild
> Built: R 3.3.0; ; 2015-04-25 20:08:25 UTC; windows
> /Henrik
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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